Concept Recognition endpoint

Concept Recognition

Deploying CARDS with docker-compose includes a ccmbioinfo/NeuralCR container. The API for the NeuralCR service is made available under /ncr/ but only if the querying user has authenticated themselves with CARDS as admin.

Annotating Text

To obtain concept annotations of a given medical text, issue a GET request to /ncr/annotate/? with the following parameters:

• text: The unstructured text to annotate.
• model: The concept recognition model trained by the given ontology. The default installation provides:
  • HPO - Human Phenotype Ontology
  • MONDO - Monarch Disease Ontology

Example

GET /ncr/annotate/?text=The+patient+has+diabetes&model=HPO

Finding Related Concepts

To obtain a ranked list of top concept ontology classes from a selected ontology that best match a given term, issue a GET request to /ncr/match/? with the following parameters:

• text: The input concept to find matches for.
• model: The concept recognition model trained by the given ontology. The default installation provides:
  • HPO - Human Phenotype Ontology
  • MONDO - Monarch Disease Ontology

Example

GET /ncr/match/?text=lung+cancer&model=HPO